Name: rs2634160
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs2634160

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:10167410 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.250349 (66265/264690, TOPMED)
G=0.247881 (34689/139942, GnomAD)
C=0.39918 (11280/28258, 14KJPN) (+ 14 more)
G=0.25731 (4860/18888, ALFA)
C=0.39797 (6670/16760, 8.3KJPN)
G=0.3285 (2104/6404, 1000G_30x)
G=0.3379 (1692/5008, 1000G)
G=0.3102 (1389/4478, Estonian)
G=0.2735 (1054/3854, ALSPAC)
G=0.2616 (970/3708, TWINSUK)
C=0.3727 (1092/2930, KOREAN)
G=0.273 (272/998, GoNL)
G=0.307 (184/600, NorthernSweden)
C=0.355 (103/290, SGDP_PRJ)
G=0.255 (55/216, Qatari)
G=0.28 (11/40, GENOME_DK)
C=0.41 (14/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: OLR1 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18888	C=0.74269	G=0.25731
European	Sub	14284	C=0.72984	G=0.27016
African	Sub	2946	C=0.8354	G=0.1646
African Others	Sub	114	C=0.798	G=0.202
African American	Sub	2832	C=0.8369	G=0.1631
Asian	Sub	112	C=0.420	G=0.580
East Asian	Sub	86	C=0.45	G=0.55
Other Asian	Sub	26	C=0.31	G=0.69
Latin American 1	Sub	146	C=0.740	G=0.260
Latin American 2	Sub	610	C=0.649	G=0.351
South Asian	Sub	98	C=0.67	G=0.33
Other	Sub	692	C=0.759	G=0.241

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.749651	G=0.250349
gnomAD - Genomes	Global	Study-wide	139942	C=0.752119	G=0.247881
gnomAD - Genomes	European	Sub	75810	C=0.72650	G=0.27350
gnomAD - Genomes	African	Sub	41924	C=0.82941	G=0.17059
gnomAD - Genomes	American	Sub	13616	C=0.72261	G=0.27739
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.8125	G=0.1875
gnomAD - Genomes	East Asian	Sub	3120	C=0.4032	G=0.5968
gnomAD - Genomes	Other	Sub	2150	C=0.7484	G=0.2516
14KJPN	JAPANESE	Study-wide	28258	C=0.39918	G=0.60082
Allele Frequency Aggregator	Total	Global	18888	C=0.74269	G=0.25731
Allele Frequency Aggregator	European	Sub	14284	C=0.72984	G=0.27016
Allele Frequency Aggregator	African	Sub	2946	C=0.8354	G=0.1646
Allele Frequency Aggregator	Other	Sub	692	C=0.759	G=0.241
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.649	G=0.351
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.740	G=0.260
Allele Frequency Aggregator	Asian	Sub	112	C=0.420	G=0.580
Allele Frequency Aggregator	South Asian	Sub	98	C=0.67	G=0.33
8.3KJPN	JAPANESE	Study-wide	16760	C=0.39797	G=0.60203
1000Genomes_30x	Global	Study-wide	6404	C=0.6715	G=0.3285
1000Genomes_30x	African	Sub	1786	C=0.8410	G=0.1590
1000Genomes_30x	Europe	Sub	1266	C=0.7370	G=0.2630
1000Genomes_30x	South Asian	Sub	1202	C=0.5691	G=0.4309
1000Genomes_30x	East Asian	Sub	1170	C=0.4197	G=0.5803
1000Genomes_30x	American	Sub	980	C=0.704	G=0.296
1000Genomes	Global	Study-wide	5008	C=0.6621	G=0.3379
1000Genomes	African	Sub	1322	C=0.8396	G=0.1604
1000Genomes	East Asian	Sub	1008	C=0.4167	G=0.5833
1000Genomes	Europe	Sub	1006	C=0.7306	G=0.2694
1000Genomes	South Asian	Sub	978	C=0.575	G=0.425
1000Genomes	American	Sub	694	C=0.705	G=0.295
Genetic variation in the Estonian population	Estonian	Study-wide	4478	C=0.6898	G=0.3102
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7265	G=0.2735
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7384	G=0.2616
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.3727	A=0.0000, G=0.6273, T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.727	G=0.273
Northern Sweden	ACPOP	Study-wide	600	C=0.693	G=0.307
SGDP_PRJ	Global	Study-wide	290	C=0.355	G=0.645
Qatari	Global	Study-wide	216	C=0.745	G=0.255
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	G=0.28
Siberian	Global	Study-wide	34	C=0.41	G=0.59

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 12	NC_000012.12:g.10167410C>A
GRCh38.p14 chr 12	NC_000012.12:g.10167410C>G
GRCh38.p14 chr 12	NC_000012.12:g.10167410C>T
GRCh37.p13 chr 12	NC_000012.11:g.10320009C>A
GRCh37.p13 chr 12	NC_000012.11:g.10320009C>G
GRCh37.p13 chr 12	NC_000012.11:g.10320009C>T
OLR1 RefSeqGene	NG_016743.1:g.9782G>T
OLR1 RefSeqGene	NG_016743.1:g.9782G>C
OLR1 RefSeqGene	NG_016743.1:g.9782G>A

Gene: OLR1, oxidized low density lipoprotein receptor 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OLR1 transcript variant 2	NM_001172632.2:c.179-453G… NM_001172632.2:c.179-453G>T	N/A	Intron Variant
OLR1 transcript variant 3	NM_001172633.2:c.179-453G… NM_001172633.2:c.179-453G>T	N/A	Intron Variant
OLR1 transcript variant 1	NM_002543.4:c.179-453G>T	N/A	Intron Variant
OLR1 transcript variant X1	XM_047428907.1:c.179-453G… XM_047428907.1:c.179-453G>T	N/A	Intron Variant
OLR1 transcript variant X2	XM_047428908.1:c.179-453G… XM_047428908.1:c.179-453G>T	N/A	Intron Variant
OLR1 transcript variant X3	XM_047428909.1:c.20-453G>T	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	A	G	T
GRCh38.p14 chr 12	NC_000012.12:g.10167410=	NC_000012.12:g.10167410C>A	NC_000012.12:g.10167410C>G	NC_000012.12:g.10167410C>T
GRCh37.p13 chr 12	NC_000012.11:g.10320009=	NC_000012.11:g.10320009C>A	NC_000012.11:g.10320009C>G	NC_000012.11:g.10320009C>T
OLR1 RefSeqGene	NG_016743.1:g.9782=	NG_016743.1:g.9782G>T	NG_016743.1:g.9782G>C	NG_016743.1:g.9782G>A
OLR1 transcript variant 2	NM_001172632.1:c.179-453=	NM_001172632.1:c.179-453G>T	NM_001172632.1:c.179-453G>C	NM_001172632.1:c.179-453G>A
OLR1 transcript variant 2	NM_001172632.2:c.179-453=	NM_001172632.2:c.179-453G>T	NM_001172632.2:c.179-453G>C	NM_001172632.2:c.179-453G>A
OLR1 transcript variant 3	NM_001172633.1:c.179-453=	NM_001172633.1:c.179-453G>T	NM_001172633.1:c.179-453G>C	NM_001172633.1:c.179-453G>A
OLR1 transcript variant 3	NM_001172633.2:c.179-453=	NM_001172633.2:c.179-453G>T	NM_001172633.2:c.179-453G>C	NM_001172633.2:c.179-453G>A
OLR1 transcript variant 1	NM_002543.3:c.179-453=	NM_002543.3:c.179-453G>T	NM_002543.3:c.179-453G>C	NM_002543.3:c.179-453G>A
OLR1 transcript variant 1	NM_002543.4:c.179-453=	NM_002543.4:c.179-453G>T	NM_002543.4:c.179-453G>C	NM_002543.4:c.179-453G>A
OLR1 transcript variant X1	XM_047428907.1:c.179-453=	XM_047428907.1:c.179-453G>T	XM_047428907.1:c.179-453G>C	XM_047428907.1:c.179-453G>A
OLR1 transcript variant X2	XM_047428908.1:c.179-453=	XM_047428908.1:c.179-453G>T	XM_047428908.1:c.179-453G>C	XM_047428908.1:c.179-453G>A
OLR1 transcript variant X3	XM_047428909.1:c.20-453=	XM_047428909.1:c.20-453G>T	XM_047428909.1:c.20-453G>C	XM_047428909.1:c.20-453G>A

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

68 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3710379	Sep 28, 2001 (100)
2	TSC-CSHL	ss5492650	Oct 10, 2002 (110)
3	SC_SNP	ss15816813	Feb 27, 2004 (120)
4	SSAHASNP	ss20863443	Apr 05, 2004 (121)
5	ABI	ss40266129	Mar 15, 2006 (126)
6	RSG_UW	ss50402324	Mar 13, 2006 (126)
7	HGSV	ss77453734	Dec 07, 2007 (129)
8	HGSV	ss82802234	Dec 15, 2007 (130)
9	HGSV	ss83113217	Dec 15, 2007 (130)
10	HUMANGENOME_JCVI	ss97285546	Feb 04, 2009 (130)
11	BGI	ss103023107	Dec 01, 2009 (131)
12	1000GENOMES	ss111469314	Jan 25, 2009 (130)
13	ENSEMBL	ss143649154	Dec 01, 2009 (131)
14	GMI	ss157097499	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss167771946	Jul 04, 2010 (132)
16	BUSHMAN	ss203537082	Jul 04, 2010 (132)
17	1000GENOMES	ss225601608	Jul 14, 2010 (132)
18	1000GENOMES	ss235819637	Jul 15, 2010 (132)
19	1000GENOMES	ss242398987	Jul 15, 2010 (132)
20	GMI	ss281270818	May 04, 2012 (137)
21	GMI	ss286504240	Apr 25, 2013 (138)
22	PJP	ss291377970	May 09, 2011 (134)
23	TISHKOFF	ss562988102	Apr 25, 2013 (138)
24	SSMP	ss658519081	Apr 25, 2013 (138)
25	EVA-GONL	ss989230796	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1078240812	Aug 21, 2014 (142)
27	1000GENOMES	ss1343886035	Aug 21, 2014 (142)
28	DDI	ss1426841123	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1576108742	Apr 01, 2015 (144)
30	EVA_DECODE	ss1598899858	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1627999041	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1670993074	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1807116358	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1932595455	Feb 12, 2016 (147)
35	JJLAB	ss2027042452	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2155364635	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2187724401	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2627999632	Nov 08, 2017 (151)
39	GRF	ss2699689471	Nov 08, 2017 (151)
40	GNOMAD	ss2907263808	Nov 08, 2017 (151)
41	SWEGEN	ss3009193001	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3027325429	Nov 08, 2017 (151)
43	CSHL	ss3349919656	Nov 08, 2017 (151)
44	URBANLAB	ss3649763811	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3676512722	Jul 13, 2019 (153)
46	EVA_DECODE	ss3693099370	Jul 13, 2019 (153)
47	ACPOP	ss3738763826	Jul 13, 2019 (153)
48	EVA	ss3750131633	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3815448933	Jul 13, 2019 (153)
50	EVA	ss3832970875	Apr 26, 2020 (154)
51	EVA	ss3840050319	Apr 26, 2020 (154)
52	EVA	ss3845533312	Apr 26, 2020 (154)
53	SGDP_PRJ	ss3877677538	Apr 26, 2020 (154)
54	KRGDB	ss3926185589	Apr 26, 2020 (154)
55	TOPMED	ss4908422043	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5205032146	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5289782411	Oct 16, 2022 (156)
58	EVA	ss5403873439	Oct 16, 2022 (156)
59	HUGCELL_USP	ss5484670755	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5586692734	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5652579199	Oct 16, 2022 (156)
62	TOMMO_GENOMICS	ss5753818417	Oct 16, 2022 (156)
63	YY_MCH	ss5813002274	Oct 16, 2022 (156)
64	EVA	ss5837579258	Oct 16, 2022 (156)
65	EVA	ss5850256706	Oct 16, 2022 (156)
66	EVA	ss5903255254	Oct 16, 2022 (156)
67	EVA	ss5943924615	Oct 16, 2022 (156)
68	EVA	ss5980721454	Oct 16, 2022 (156)
69	1000Genomes	NC_000012.11 - 10320009	Oct 12, 2018 (152)
70	1000Genomes_30x	NC_000012.12 - 10167410	Oct 16, 2022 (156)
71	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 10320009	Oct 12, 2018 (152)
72	Genetic variation in the Estonian population	NC_000012.11 - 10320009	Oct 12, 2018 (152)
73	The Danish reference pan genome	NC_000012.11 - 10320009	Apr 26, 2020 (154)
74	gnomAD - Genomes	NC_000012.12 - 10167410	Apr 26, 2021 (155)
75	Genome of the Netherlands Release 5	NC_000012.11 - 10320009	Apr 26, 2020 (154)
76	KOREAN population from KRGDB	NC_000012.11 - 10320009	Apr 26, 2020 (154)
77	Northern Sweden	NC_000012.11 - 10320009	Jul 13, 2019 (153)
78	Qatari	NC_000012.11 - 10320009	Apr 26, 2020 (154)
79	SGDP_PRJ	NC_000012.11 - 10320009	Apr 26, 2020 (154)
80	Siberian	NC_000012.11 - 10320009	Apr 26, 2020 (154)
81	8.3KJPN	NC_000012.11 - 10320009	Apr 26, 2021 (155)
82	14KJPN	NC_000012.12 - 10167410	Oct 16, 2022 (156)
83	TopMed	NC_000012.12 - 10167410	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000012.11 - 10320009	Oct 12, 2018 (152)
85	ALFA	NC_000012.12 - 10167410	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs4088829	Dec 16, 2002 (110)
rs34470942	May 23, 2006 (127)
rs58192636	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
33362983, ss3926185589	NC_000012.11:10320008:C:A	NC_000012.12:10167409:C:A	(self)
ss77453734, ss82802234, ss83113217	NC_000012.9:10211275:C:G	NC_000012.12:10167409:C:G	(self)
ss111469314, ss167771946, ss203537082, ss281270818, ss286504240, ss291377970, ss1598899858	NC_000012.10:10211275:C:G	NC_000012.12:10167409:C:G	(self)
56592426, 31422136, 22250970, 2840325, 14019381, 33362983, 12048691, 14637385, 29694518, 7880989, 63001453, 31422136, ss225601608, ss235819637, ss242398987, ss562988102, ss658519081, ss989230796, ss1078240812, ss1343886035, ss1426841123, ss1576108742, ss1627999041, ss1670993074, ss1807116358, ss1932595455, ss2027042452, ss2155364635, ss2627999632, ss2699689471, ss2907263808, ss3009193001, ss3349919656, ss3676512722, ss3738763826, ss3750131633, ss3832970875, ss3840050319, ss3877677538, ss3926185589, ss5205032146, ss5403873439, ss5652579199, ss5837579258, ss5943924615, ss5980721454	NC_000012.11:10320008:C:G	NC_000012.12:10167409:C:G	(self)
74218669, 399054101, 87655521, 123967700, 12542912039, ss2187724401, ss3027325429, ss3649763811, ss3693099370, ss3815448933, ss3845533312, ss4908422043, ss5289782411, ss5484670755, ss5586692734, ss5753818417, ss5813002274, ss5850256706, ss5903255254	NC_000012.12:10167409:C:G	NC_000012.12:10167409:C:G	(self)
ss15816813, ss20863443	NT_009714.16:3078982:C:G	NC_000012.12:10167409:C:G	(self)
ss3710379, ss5492650, ss40266129, ss50402324, ss97285546, ss103023107, ss143649154, ss157097499	NT_009714.17:3080132:C:G	NC_000012.12:10167409:C:G	(self)
33362983, ss3926185589	NC_000012.11:10320008:C:T	NC_000012.12:10167409:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs2634160

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
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NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2634160